revdep check results update, with cytominer fixed. [ci skip]

vkd0726 · Apr 2, 2019 · 8761401 · 8761401
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diff --git a/revdep/README.md b/revdep/README.md
@@ -5,12 +5,12 @@
 |version  |R version 3.5.3 (2019-03-11) |
 |os       |macOS Mojave 10.14.4         |
 |system   |x86_64, darwin15.6.0         |
-|ui       |X11                          |
+|ui       |RStudio                      |
 |language |(EN)                         |
 |collate  |en_US.UTF-8                  |
 |ctype    |en_US.UTF-8                  |
 |tz       |Europe/Paris                 |
-|date     |2019-04-01                   |
+|date     |2019-04-02                   |
 
 # Dependencies
 
@@ -87,39 +87,37 @@
 |[ZeligEI](problems.md#zeligei)                       |0.1-2    |1     |        |     |[cran/ZeligEI](https://github.com/cran/ZeligEI)                       |
 |[zeligverse](problems.md#zeligverse)                 |0.1.1    |1     |        |     |[cran/zeligverse](https://github.com/cran/zeligverse)                 |
 
-## Broken (31)
-
-|package                                                |version  |error  |warning |note |source                                                                  |
-|:------------------------------------------------------|:--------|:------|:-------|:----|:-----------------------------------------------------------------------|
-|[broomExtra](problems.md#broomextra)                   |0.0.1    |__+2__ |        |     |[cran/broomExtra](https://github.com/cran/broomExtra)                   |
-|[ClinReport](problems.md#clinreport)                   |0.9.1.11 |__+1__ |__+1__  |1    |[cran/ClinReport](https://github.com/cran/ClinReport)                   |
-|[coalitions](problems.md#coalitions)                   |0.6.5    |__+2__ |__+1__  |     |[cran/coalitions](https://github.com/cran/coalitions)                   |
-|[compareDF](problems.md#comparedf)                     |1.7.1    |__+1__ |        |1    |[cran/compareDF](https://github.com/cran/compareDF)                     |
-|[corrr](problems.md#corrr)                             |0.3.1    |       |__+1__  |     |[cran/corrr](https://github.com/cran/corrr)                             |
-|[cytominer](problems.md#cytominer)                     |0.1.0    |__+2__ |__+1__  |     |[cran/cytominer](https://github.com/cran/cytominer)                     |
-|[dbplyr](problems.md#dbplyr)                           |1.3.0    |__+1__ |        |     |[cran/dbplyr](https://github.com/cran/dbplyr)                           |
-|[desctable](problems.md#desctable)                     |0.1.5    |       |__+1__  |     |[cran/desctable](https://github.com/cran/desctable)                     |
-|[ELMER](problems.md#elmer)                             |2.4.4    |1      |1       |3    |[cran/ELMER](https://github.com/cran/ELMER)                             |
-|[FindMyFriends](problems.md#findmyfriends)             |1.10.0   |1      |1       |2    |[cran/FindMyFriends](https://github.com/cran/FindMyFriends)             |
-|[GFE](problems.md#gfe)                                 |0.1.0    |__+1__ |        |     |[cran/GFE](https://github.com/cran/GFE)                                 |
-|[grasp2db](problems.md#grasp2db)                       |1.1.0    |1      |3       |4    |[cran/grasp2db](https://github.com/cran/grasp2db)                       |
-|[groupedstats](problems.md#groupedstats)               |0.0.6    |__+1__ |        |     |[cran/groupedstats](https://github.com/cran/groupedstats)               |
-|[healthcareai](problems.md#healthcareai)               |2.3.0    |__+1__ |        |     |[cran/healthcareai](https://github.com/cran/healthcareai)               |
-|[HTSSIP](problems.md#htssip)                           |1.4.0    |1      |        |1    |[cran/HTSSIP](https://github.com/cran/HTSSIP)                           |
-|[InjurySeverityScore](problems.md#injuryseverityscore) |0.0.0.1  |__+1__ |        |     |[cran/InjurySeverityScore](https://github.com/cran/InjurySeverityScore) |
-|[kayadata](problems.md#kayadata)                       |0.4.0    |__+1__ |__+1__  |     |[cran/kayadata](https://github.com/cran/kayadata)                       |
-|[modeldb](problems.md#modeldb)                         |0.1.2    |       |__+1__  |     |[cran/modeldb](https://github.com/cran/modeldb)                         |
-|[MonetDBLite](problems.md#monetdblite)                 |0.6.0    |__+1__ |        |1    |[cran/MonetDBLite](https://github.com/cran/MonetDBLite)                 |
-|[perturbatr](problems.md#perturbatr)                   |1.0.0    |__+1__ |        |     |[cran/perturbatr](https://github.com/cran/perturbatr)                   |
-|[pmc](problems.md#pmc)                                 |1.0.3    |1      |        |     |[cran/pmc](https://github.com/cran/pmc)                                 |
-|[QuaternaryProd](problems.md#quaternaryprod)           |1.14.0   |1      |        |1    |[cran/QuaternaryProd](https://github.com/cran/QuaternaryProd)           |
-|[radiant.basics](problems.md#radiantbasics)            |0.9.9    |__+2__ |        |     |[cran/radiant.basics](https://github.com/cran/radiant.basics)           |
-|[radiant.data](problems.md#radiantdata)                |0.9.9    |__+1__ |        |     |[cran/radiant.data](https://github.com/cran/radiant.data)               |
-|[radiant.model](problems.md#radiantmodel)              |0.9.9    |__+1__ |        |     |[cran/radiant.model](https://github.com/cran/radiant.model)             |
-|[rubias](problems.md#rubias)                           |0.2.0    |1      |        |1    |[cran/rubias](https://github.com/cran/rubias)                           |
-|[ruler](problems.md#ruler)                             |0.2.0    |__+2__ |        |     |[cran/ruler](https://github.com/cran/ruler)                             |
-|[strapgod](problems.md#strapgod)                       |0.0.1    |__+1__ |        |     |[cran/strapgod](https://github.com/cran/strapgod)                       |
-|[survivalAnalysis](problems.md#survivalanalysis)       |0.1.1    |__+1__ |__+1__  |     |[cran/survivalAnalysis](https://github.com/cran/survivalAnalysis)       |
-|[TCGAbiolinks](problems.md#tcgabiolinks)               |2.8.4    |1      |1       |2    |[cran/TCGAbiolinks](https://github.com/cran/TCGAbiolinks)               |
-|[XBSeq](problems.md#xbseq)                             |1.12.0   |1      |        |2    |[cran/XBSeq](https://github.com/cran/XBSeq)                             |
+## Broken (30)
 
+|package                                                |version  |error     |warning |note |source                                                                  |
+|:------------------------------------------------------|:--------|:---------|:-------|:----|:-----------------------------------------------------------------------|
+|[broomExtra](problems.md#broomextra)                   |0.0.1    |-1 __+2__ |        |     |[cran/broomExtra](https://github.com/cran/broomExtra)                   |
+|[ClinReport](problems.md#clinreport)                   |0.9.1.11 |1         |__+1__  |1    |[cran/ClinReport](https://github.com/cran/ClinReport)                   |
+|[coalitions](problems.md#coalitions)                   |0.6.5    |__+2__    |__+1__  |     |[cran/coalitions](https://github.com/cran/coalitions)                   |
+|[compareDF](problems.md#comparedf)                     |1.7.1    |__+1__    |        |1    |[cran/compareDF](https://github.com/cran/compareDF)                     |
+|[corrr](problems.md#corrr)                             |0.3.1    |          |__+1__  |     |[cran/corrr](https://github.com/cran/corrr)                             |
+|[dbplyr](problems.md#dbplyr)                           |1.3.0    |__+1__    |        |     |[cran/dbplyr](https://github.com/cran/dbplyr)                           |
+|[desctable](problems.md#desctable)                     |0.1.5    |          |__+1__  |     |[cran/desctable](https://github.com/cran/desctable)                     |
+|[ELMER](problems.md#elmer)                             |2.4.4    |1         |1       |3    |[cran/ELMER](https://github.com/cran/ELMER)                             |
+|[FindMyFriends](problems.md#findmyfriends)             |1.10.0   |1         |1       |2    |[cran/FindMyFriends](https://github.com/cran/FindMyFriends)             |
+|[GFE](problems.md#gfe)                                 |0.1.0    |__+1__    |        |     |[cran/GFE](https://github.com/cran/GFE)                                 |
+|[grasp2db](problems.md#grasp2db)                       |1.1.0    |1         |3       |4    |[cran/grasp2db](https://github.com/cran/grasp2db)                       |
+|[groupedstats](problems.md#groupedstats)               |0.0.6    |__+1__    |        |     |[cran/groupedstats](https://github.com/cran/groupedstats)               |
+|[healthcareai](problems.md#healthcareai)               |2.3.0    |__+1__    |        |     |[cran/healthcareai](https://github.com/cran/healthcareai)               |
+|[HTSSIP](problems.md#htssip)                           |1.4.0    |1         |        |1    |[cran/HTSSIP](https://github.com/cran/HTSSIP)                           |
+|[InjurySeverityScore](problems.md#injuryseverityscore) |0.0.0.1  |__+1__    |        |     |[cran/InjurySeverityScore](https://github.com/cran/InjurySeverityScore) |
+|[kayadata](problems.md#kayadata)                       |0.4.0    |__+1__    |__+1__  |     |[cran/kayadata](https://github.com/cran/kayadata)                       |
+|[modeldb](problems.md#modeldb)                         |0.1.2    |          |__+1__  |     |[cran/modeldb](https://github.com/cran/modeldb)                         |
+|[MonetDBLite](problems.md#monetdblite)                 |0.6.0    |__+1__    |        |1    |[cran/MonetDBLite](https://github.com/cran/MonetDBLite)                 |
+|[perturbatr](problems.md#perturbatr)                   |1.0.0    |__+1__    |        |     |[cran/perturbatr](https://github.com/cran/perturbatr)                   |
+|[pmc](problems.md#pmc)                                 |1.0.3    |1         |        |     |[cran/pmc](https://github.com/cran/pmc)                                 |
+|[QuaternaryProd](problems.md#quaternaryprod)           |1.14.0   |1         |        |1    |[cran/QuaternaryProd](https://github.com/cran/QuaternaryProd)           |
+|[radiant.basics](problems.md#radiantbasics)            |0.9.9    |__+2__    |        |     |[cran/radiant.basics](https://github.com/cran/radiant.basics)           |
+|[radiant.data](problems.md#radiantdata)                |0.9.9    |__+1__    |        |     |[cran/radiant.data](https://github.com/cran/radiant.data)               |
+|[radiant.model](problems.md#radiantmodel)              |0.9.9    |__+1__    |        |     |[cran/radiant.model](https://github.com/cran/radiant.model)             |
+|[rubias](problems.md#rubias)                           |0.2.0    |1         |        |1    |[cran/rubias](https://github.com/cran/rubias)                           |
+|[ruler](problems.md#ruler)                             |0.2.0    |__+2__    |        |     |[cran/ruler](https://github.com/cran/ruler)                             |
+|[strapgod](problems.md#strapgod)                       |0.0.1    |__+1__    |        |     |[cran/strapgod](https://github.com/cran/strapgod)                       |
+|[survivalAnalysis](problems.md#survivalanalysis)       |0.1.1    |__+1__    |__+1__  |     |[cran/survivalAnalysis](https://github.com/cran/survivalAnalysis)       |
+|[TCGAbiolinks](problems.md#tcgabiolinks)               |2.8.4    |1         |1       |2    |[cran/TCGAbiolinks](https://github.com/cran/TCGAbiolinks)               |
+|[XBSeq](problems.md#xbseq)                             |1.12.0   |1         |        |2    |[cran/XBSeq](https://github.com/cran/XBSeq)                             |
diff --git a/revdep/problems.md b/revdep/problems.md
@@ -52,38 +52,20 @@ Version: 0.0.1
       Execution halted
     ```
 
+## Newly fixed
+
+*   checking whether package ‘broomExtra’ can be installed ... ERROR
+    ```
+    Installation failed.
+    See ‘/Users/romainfrancois/git/dplyr-revdep/dplyr/revdep/checks.noindex/broomExtra/old/broomExtra.Rcheck/00install.out’ for details.
+    ```
+
 # ClinReport
 
 Version: 0.9.1.11
 
 ## Newly broken
 
-*   checking examples ... ERROR
-    ```
-    ...
-    > 
-    > 
-    > # Load the data
-    > 
-    > data(data)
-    > 
-    > # The default statistics are given here:
-    > 
-    > tab1=report.quanti(data=data,y="y_numeric",x1="GROUP",total=TRUE,subjid="SUBJID")
-    > 
-    > # Define the function corresponding to the coefficient of variation for example
-    > 
-    > cv=function(y) sd(y,na.rm=TRUE)/mean(y,na.rm=TRUE)
-    > 
-    > # We use the add.stat function to add CV at the second row:
-    > 
-    > tab1.cv=add.stat(tab1,data,func.stat=cv,func.stat.name="Coef. Var",
-    + pos=2)
-    Error in func.stat(y_numeric) : could not find function "func.stat"
-    Calls: add.stat ... summarise -> summarise.tbl_df -> summarise_impl -> <Anonymous>
-    Execution halted
-    ```
-
 *   checking re-building of vignette outputs ... WARNING
     ```
     ...
@@ -112,6 +94,32 @@ Version: 0.9.1.11
 
 ## In both
 
+*   checking examples ... ERROR
+    ```
+    ...
+    > 
+    > 
+    > # Load the data
+    > 
+    > data(data)
+    > 
+    > # The default statistics are given here:
+    > 
+    > tab1=report.quanti(data=data,y="y_numeric",x1="GROUP",total=TRUE,subjid="SUBJID")
+    > 
+    > # Define the function corresponding to the coefficient of variation for example
+    > 
+    > cv=function(y) sd(y,na.rm=TRUE)/mean(y,na.rm=TRUE)
+    > 
+    > # We use the add.stat function to add CV at the second row:
+    > 
+    > tab1.cv=add.stat(tab1,data,func.stat=cv,func.stat.name="Coef. Var",
+    + pos=2)
+    Error in func.stat(y_numeric) : could not find function "func.stat"
+    Calls: add.stat ... summarise -> summarise.tbl_df -> summarise_impl -> <Anonymous>
+    Execution halted
+    ```
+
 *   checking dependencies in R code ... NOTE
     ```
     Namespaces in Imports field not imported from:
@@ -248,70 +256,6 @@ Version: 0.3.1
     Execution halted
     ```
 
-# cytominer
-
-Version: 0.1.0
-
-## Newly broken
-
-*   checking examples ... ERROR
-    ```
-    ...
-    
-    > ### Name: normalize
-    > ### Title: Normalize observation variables.
-    > ### Aliases: normalize
-    > 
-    > ### ** Examples
-    > 
-    > suppressMessages(suppressWarnings(library(magrittr)))
-    > population <- tibble::data_frame(
-    +    Metadata_group = c("control", "control", "control", "control",
-    +                       "experiment", "experiment", "experiment", "experiment"),
-    +    Metadata_batch = c("a", "a", "b", "b", "a", "a", "b", "b"),
-    +    AreaShape_Area = c(10, 12, 15, 16, 8, 8, 7, 7)
-    +  )
-    > variables <- c('AreaShape_Area')
-    > strata <- c('Metadata_batch')
-    > sample <- population %>% dplyr::filter(Metadata_group == 'control')
-    > cytominer::normalize(population, variables, strata, sample, operation = "standardize")
-    Error in mean(., na.rm = TRUE) : object '.' not found
-    Calls: <Anonymous> ... summarise.tbl_df -> summarise_impl -> <Anonymous> -> eval_tidy -> mean
-    Execution halted
-    ```
-
-*   checking tests ...
-    ```
-     ERROR
-    Running the tests in ‘tests/testthat.R’ failed.
-    Last 13 lines of output:
-      32: eval_bare(call, env)
-      33: (function (...) 
-         eval_tidy(~mean(.)))(x)
-      34: eval_tidy(~mean(.))
-      35: mean(.)
-      
-      ══ testthat results  ═══════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════
-      OK: 28 SKIPPED: 0 FAILED: 4
-      1. Error: `aggregate` aggregates data (@test-aggregate.R#37) 
-      2. Error: cytominer can process dataset with a normalized schema (@test-cytominer.R#71) 
-      3. Error: cytominer can process dataset with a CellProfiler schema (@test-cytominer.R#227) 
-      4. Error: `normalize' normalizes data (@test-normalize.R#49) 
-      
-      Error: testthat unit tests failed
-      Execution halted
-    ```
-
-*   checking re-building of vignette outputs ... WARNING
-    ```
-    Error in re-building vignettes:
-      ...
-    Quitting from lines 149-165 (cytominer-pipeline.Rmd) 
-    Error: processing vignette 'cytominer-pipeline.Rmd' failed with diagnostics:
-    object '.' not found
-    Execution halted
-    ```
-
 # dbplyr
 
 Version: 1.3.0